SnpEff: Variant analysis

Contents Summary
Variant rate by chromosome
Variants by type
Number of variants by impact
Number of variants by functional class
Number of variants by effect
Quality histogram
InDel length histogram
Base variant table
Transition vs transversions (ts/tv)
Allele frequency
Allele Count
Codon change table
Amino acid change table
Chromosome variants plots
Details by gene

Summary

Genome brucella_suis_cita_364

Date 2025-02-19 16:50

SnpEff version
SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani

Command line arguments
SnpEff -csvStats CRG2_struct.snpEff_summary.csv -htmlStats CRG2_struct.snpEff_summary.html brucella_suis_cita_364 CRG2_struct.vcf

Warnings 57

Errors 2

Number of lines (input file) 21

Number of variants (before filter) 18

Number of not variants
(i.e. reference equals alternative) 0

Number of variants processed
(i.e. after filter and non-variants) 18

Number of known variants
(i.e. non-empty ID) 18 ( 100% )

Number of multi-allelic VCF entries
(i.e. more than two alleles) 0

Number of effects 391

Genome total length 3,328,972

Genome effective length 3,328,972

Variant rate 1 variant every 184,942 bases

Variants rate details

Chromosome Length Variants Variants rate

NZ_CP007697.1 1,927,594 13 148,276

NZ_CP007698.1 1,401,378 5 280,275

Total 3,328,972 18 184,942

Chromosome	Length	Variants	Variants rate
NZ_CP007697.1	1,927,594	13	148,276
NZ_CP007698.1	1,401,378	5	280,275
Total	3,328,972	18	184,942

Number variants by type

Type Total

SNP 0

MNP 0

INS 0

DEL 16

MIXED 0

INV 0

DUP 2

BND 0

INTERVAL 0

Total 18

Type	Total
SNP	0
MNP	0
INS	0
DEL	16
MIXED	0
INV	0
DUP	2
BND	0
INTERVAL	0
Total	18

Number of effects by impact

Type (alphabetical order) Count Percent

HIGH 194 49.616%

MODERATE 5 1.279%

MODIFIER 192 49.105%

Type (alphabetical order)	Count	Percent
HIGH	194	49.616%
MODERATE	5	1.279%
MODIFIER	192	49.105%

Number of effects by functional class

Type (alphabetical order) Count Percent

Missense / Silent ratio: 0

Number of effects by type and region

Type Region

Type (alphabetical order) Count Percent

bidirectional_gene_fusion 5 1.222%

chromosome_number_variation 2 0.489%

conservative_inframe_deletion 6 1.467%

downstream_gene_variant 77 18.826%

duplication 3 0.733%

exon_loss_variant 4 0.978%

feature_ablation 47 11.491%

frameshift_variant 9 2.2%

gene_fusion 6 1.467%

intragenic_variant 7 1.711%

intron_variant 17 4.156%

splice_region_variant 6 1.467%

start_lost 7 1.711%

stop_lost 5 1.222%

transcript_ablation 117 28.606%

upstream_gene_variant 91 22.249%

Type (alphabetical order) Count Percent

CHROMOSOME 2 0.512%

DOWNSTREAM 77 19.693%

EXON 19 4.859%

GENE 60 15.345%

INTRON 17 4.348%

TRANSCRIPT 125 31.969%

UPSTREAM 91 23.274%

Quality:

Insertions and deletions length:

	
		 Min 1  
		 Max 1  
		 Mean 1  
		 Median 1  
		 Standard deviation 0  
		 Values 1  
		 Count 16

Base changes (SNPs)

A C G T

A 0 0 0 0

C 0 0 0 0

G 0 0 0 0

T 0 0 0 0

	A	C	G	T
A	0	0	0	0
C	0	0	0	0
G	0	0	0	0
T	0	0	0	0

Ts/Tv (transitions / transversions)

Note: Only SNPs are used for this statistic.
Note: This Ts/Tv ratio is a 'raw' ratio (ratio of observed events).

Transitions	0
Transversions	0
Ts/Tv ratio	0

All variants:

No results available (empty input?)

Only known variants (i.e. the ones having a non-empty ID field):

No results available (empty input?)

Allele frequency

Allele Count

Min	1
Max	1
Mean	1
Median	1
Standard deviation	0
Values	1
Count	21

Hom/Het per sample

Sample_names 
Reference 
Het 
Hom 
Missing

Codon changes

How to read this table:
- Rows are reference codons and columns are changed codons. E.g. Row 'AAA' column 'TAA' indicates how many 'AAA' codons have been replaced by 'TAA' codons.
- Red background colors indicate that more changes happened (heat-map).
- Diagonals are indicated using grey background color
- WARNING: This table may include different translation codon tables (e.g. mamalian DNA and mitochondrial DNA).

- AAA AAC AAG AAT ACA ACC ACG ACT AGA AGC AGG AGT ATA ATC ATG ATT CAA CAC CAG CAT CCA CCC CCG CCT CGA CGC CGG CGT CTA CTC CTG CTT GAA GAC GAG GAT GCA GCC GCG GCT GGA GGC GGG GGT GTA GTC GTG GTT TAA TAC TAG TAT TCA TCC TCG TCT TGA TGC TGG TGT TTA TTC TTG TTT

-

AAA 21

AAC 14

AAG 74

AAT 30

ACA 7

ACC 29

ACG 21

ACT 4

AGA 8

AGC 19

AGG 11

AGT 3

ATA 8

ATC 54

ATG 36

ATT 39

CAA 14

CAC 22

CAG 38

CAT 17

CCA 10

CCC 16

CCG 41

CCT 10

CGA 8

CGC 54

CGG 17

CGT 25

CTA 8

CTC 18

CTG 62

CTT 49

GAA 75

GAC 65

GAG 57

GAT 56

GCA 36

GCC 75

GCG 80

GCT 48

GGA 14

GGC 88

GGG 19

GGT 15

GTA 5

GTC 27

GTG 37

GTT 32

TAA 2

TAC 20

TAG 1

TAT 29

TCA 8

TCC 16

TCG 27

TCT 4

TGA 2

TGC 13

TGG 24

TGT 4

TTA 2

TTC 54

TTG 22

TTT 25

Amino acid changes

How to read this table:
- Rows are reference amino acids and columns are changed amino acids. E.g. Row 'A' column 'E' indicates how many 'A' amino acids have been replaced by 'E' amino acids.
- Red background colors indicate that more changes happened (heat-map).
- Diagonals are indicated using grey background color
- WARNING: This table may include different translation codon tables (e.g. mamalian DNA and mitochondrial DNA).

* - A C D E F G H I K L M N P Q R S T V W Y

* 5

-

A 239

C 17

D 121

E 132

F 79

G 136

H 39

I 101

K 95

L 161

M 36

N 44

P 77

Q 52

R 123

S 77

T 61

V 101

W 24

Y 49

Variants by chromosome

		

		NZ_CP007697.1, Position,0,10000,20000,30000,40000,50000,60000,70000,80000,90000,100000,110000,120000,130000,140000,150000,160000,170000,180000,190000,200000,210000,220000,230000,240000,250000,260000,270000,280000,290000,300000,310000,320000,330000,340000,350000,360000,370000,380000,390000,400000,410000,420000,430000,440000,450000,460000,470000,480000,490000,500000,510000,520000,530000,540000,550000,560000,570000,580000,590000,600000,610000,620000,630000,640000,650000,660000,670000,680000,690000,700000,710000,720000,730000,740000,750000,760000,770000,780000,790000,800000,810000,820000,830000,840000,850000,860000,870000,880000,890000,900000,910000,920000,930000,940000,950000,960000,970000,980000,990000,1000000,1010000,1020000,1030000,1040000,1050000,1060000,1070000,1080000,1090000,1100000,1110000,1120000,1130000,1140000,1150000,1160000,1170000,1180000,1190000,1200000,1210000,1220000,1230000,1240000,1250000,1260000,1270000,1280000,1290000,1300000,1310000,1320000,1330000,1340000,1350000,1360000,1370000,1380000,1390000,1400000,1410000,1420000,1430000,1440000,1450000,1460000,1470000,1480000,1490000,1500000,1510000,1520000,1530000,1540000,1550000,1560000,1570000,1580000,1590000,1600000,1610000,1620000,1630000,1640000,1650000,1660000,1670000,1680000,1690000,1700000,1710000,1720000,1730000,1740000,1750000,1760000,1770000,1780000,1790000,1800000,1810000,1820000,1830000,1840000,1850000,1860000,1870000,1880000,1890000,1900000,1910000,1920000
NZ_CP007697.1,Count,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,2,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,1,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0

		

		NZ_CP007698.1, Position,0,10000,20000,30000,40000,50000,60000,70000,80000,90000,100000,110000,120000,130000,140000,150000,160000,170000,180000,190000,200000,210000,220000,230000,240000,250000,260000,270000,280000,290000,300000,310000,320000,330000,340000,350000,360000,370000,380000,390000,400000,410000,420000,430000,440000,450000,460000,470000,480000,490000,500000,510000,520000,530000,540000,550000,560000,570000,580000,590000,600000,610000,620000,630000,640000,650000,660000,670000,680000,690000,700000,710000,720000,730000,740000,750000,760000,770000,780000,790000,800000,810000,820000,830000,840000,850000,860000,870000,880000,890000,900000,910000,920000,930000,940000,950000,960000,970000,980000,990000,1000000,1010000,1020000,1030000,1040000,1050000,1060000,1070000,1080000,1090000,1100000,1110000,1120000,1130000,1140000,1150000,1160000,1170000,1180000,1190000,1200000,1210000,1220000,1230000,1240000,1250000,1260000,1270000,1280000,1290000,1300000,1310000,1320000,1330000,1340000,1350000,1360000,1370000,1380000,1390000,1400000
NZ_CP007698.1,Count,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,1,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0

Details by gene

Here you can find a tab-separated table.

Genome	brucella_suis_cita_364
Date	2025-02-19 16:50
SnpEff version	SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Command line arguments	SnpEff -csvStats CRG2_struct.snpEff_summary.csv -htmlStats CRG2_struct.snpEff_summary.html brucella_suis_cita_364 CRG2_struct.vcf
Warnings	57
Errors	2
Number of lines (input file)	21
Number of variants (before filter)	18
Number of not variants (i.e. reference equals alternative)	0
Number of variants processed (i.e. after filter and non-variants)	18
Number of known variants (i.e. non-empty ID)	18 ( 100% )
Number of multi-allelic VCF entries (i.e. more than two alleles)	0
Number of effects	391
Genome total length	3,328,972
Genome effective length	3,328,972
Variant rate	1 variant every 184,942 bases

	-	AAA	AAC	AAG	AAT	ACA	ACC	ACG	ACT	AGA	AGC	AGG	AGT	ATA	ATC	ATG	ATT	CAA	CAC	CAG	CAT	CCA	CCC	CCG	CCT	CGA	CGC	CGG	CGT	CTA	CTC	CTG	CTT	GAA	GAC	GAG	GAT	GCA	GCC	GCG	GCT	GGA	GGC	GGG	GGT	GTA	GTC	GTG	GTT	TAA	TAC	TAG	TAT	TCA	TCC	TCG	TCT	TGA	TGC	TGG	TGT	TTA	TTC	TTG	TTT
-
AAA	21
AAC	14
AAG	74
AAT	30
ACA	7
ACC	29
ACG	21
ACT	4
AGA	8
AGC	19
AGG	11
AGT	3
ATA	8
ATC	54
ATG	36
ATT	39
CAA	14
CAC	22
CAG	38
CAT	17
CCA	10
CCC	16
CCG	41
CCT	10
CGA	8
CGC	54
CGG	17
CGT	25
CTA	8
CTC	18
CTG	62
CTT	49
GAA	75
GAC	65
GAG	57
GAT	56
GCA	36
GCC	75
GCG	80
GCT	48
GGA	14
GGC	88
GGG	19
GGT	15
GTA	5
GTC	27
GTG	37
GTT	32
TAA	2
TAC	20
TAG	1
TAT	29
TCA	8
TCC	16
TCG	27
TCT	4
TGA	2
TGC	13
TGG	24
TGT	4
TTA	2
TTC	54
TTG	22
TTT	25

	*	-	A	C	D	E	F	G	H	I	K	L	M	N	P	Q	R	S	T	V	W	Y
*		5
-
A		239
C		17
D		121
E		132
F		79
G		136
H		39
I		101
K		95
L		161
M		36
N		44
P		77
Q		52
R		123
S		77
T		61
V		101
W		24
Y		49

	-	AAA	AAC	AAG	AAT	ACA	ACC	ACG	ACT	AGA	AGC	AGG	AGT	ATA	ATC	ATG	ATT	CAA	CAC	CAG	CAT	CCA	CCC	CCG	CCT	CGA	CGC	CGG	CGT	CTA	CTC	CTG	CTT	GAA	GAC	GAG	GAT	GCA	GCC	GCG	GCT	GGA	GGC	GGG	GGT	GTA	GTC	GTG	GTT	TAA	TAC	TAG	TAT	TCA	TCC	TCG	TCT	TGA	TGC	TGG	TGT	TTA	TTC	TTG	TTT
-
AAA	21
AAC	14
AAG	74
AAT	30
ACA	7
ACC	29
ACG	21
ACT	4
AGA	8
AGC	19
AGG	11
AGT	3
ATA	8
ATC	54
ATG	36
ATT	39
CAA	14
CAC	22
CAG	38
CAT	17
CCA	10
CCC	16
CCG	41
CCT	10
CGA	8
CGC	54
CGG	17
CGT	25
CTA	8
CTC	18
CTG	62
CTT	49
GAA	75
GAC	65
GAG	57
GAT	56
GCA	36
GCC	75
GCG	80
GCT	48
GGA	14
GGC	88
GGG	19
GGT	15
GTA	5
GTC	27
GTG	37
GTT	32
TAA	2
TAC	20
TAG	1
TAT	29
TCA	8
TCC	16
TCG	27
TCT	4
TGA	2
TGC	13
TGG	24
TGT	4
TTA	2
TTC	54
TTG	22
TTT	25

	*	-	A	C	D	E	F	G	H	I	K	L	M	N	P	Q	R	S	T	V	W	Y
*		5
-
A		239
C		17
D		121
E		132
F		79
G		136
H		39
I		101
K		95
L		161
M		36
N		44
P		77
Q		52
R		123
S		77
T		61
V		101
W		24
Y		49

	-	AAA	AAC	AAG	AAT	ACA	ACC	ACG	ACT	AGA	AGC	AGG	AGT	ATA	ATC	ATG	ATT	CAA	CAC	CAG	CAT	CCA	CCC	CCG	CCT	CGA	CGC	CGG	CGT	CTA	CTC	CTG	CTT	GAA	GAC	GAG	GAT	GCA	GCC	GCG	GCT	GGA	GGC	GGG	GGT	GTA	GTC	GTG	GTT	TAA	TAC	TAG	TAT	TCA	TCC	TCG	TCT	TGA	TGC	TGG	TGT	TTA	TTC	TTG	TTT
-
AAA	21
AAC	14
AAG	74
AAT	30
ACA	7
ACC	29
ACG	21
ACT	4
AGA	8
AGC	19
AGG	11
AGT	3
ATA	8
ATC	54
ATG	36
ATT	39
CAA	14
CAC	22
CAG	38
CAT	17
CCA	10
CCC	16
CCG	41
CCT	10
CGA	8
CGC	54
CGG	17
CGT	25
CTA	8
CTC	18
CTG	62
CTT	49
GAA	75
GAC	65
GAG	57
GAT	56
GCA	36
GCC	75
GCG	80
GCT	48
GGA	14
GGC	88
GGG	19
GGT	15
GTA	5
GTC	27
GTG	37
GTT	32
TAA	2
TAC	20
TAG	1
TAT	29
TCA	8
TCC	16
TCG	27
TCT	4
TGA	2
TGC	13
TGG	24
TGT	4
TTA	2
TTC	54
TTG	22
TTT	25

	*	-	A	C	D	E	F	G	H	I	K	L	M	N	P	Q	R	S	T	V	W	Y
*		5
-
A		239
C		17
D		121
E		132
F		79
G		136
H		39
I		101
K		95
L		161
M		36
N		44
P		77
Q		52
R		123
S		77
T		61
V		101
W		24
Y		49